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Genomic Innovations- Orthology Paralogy. Genomic innovation.

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Presentation on theme: "Genomic Innovations- Orthology Paralogy. Genomic innovation."— Presentation transcript:

1 Genomic Innovations- Orthology Paralogy

2 Genomic innovation

3 Moore, Current opinion in Plant Biology, 2005

4 Genomic innovation- Paralogy Cotton, Methods in Enzymology, 2005

5 Homology, Orthology, Paralogy Homology is a relation between a pair of genes that share a common ancestor. Orthology is a relation defined over a pair of homologous genes, where the two genes have emerged through a speciation event Paralogy is a relation defined over a pair of homologous genes that have emerged through a gene duplication A.M. Altenhoff and C. Dessimoz, Inferring Orthology and Paralogy

6 In and out Paralogy In-paralogy if they are paralogs and duplicated after the speciation event of reference Out-paralogy if the duplication event through which they are related to each other predates the speciation event of reference

7 Ensembl A joint project between EMBL - European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) A genome browser for the retrieval of genomic information

8 BioMart BioMart is a search engine that can find multiple terms and put them into a table format. Such as: human gene (IDs), chromosome and base pair position

9 BioMart

10 1)Choose the species of interest (Dataset) 2)Decide what you would like to know about the genes (Attributes) (sequences, IDs, description…) 1)Decide on a smaller geneset using Filters. (enter IDs, choose a region …) How does BioMart work?

11 Choose the species of interest Choose the gene set Choose the information you want to view BioMart

12 Choose the species of interest: Homo sapiens is the default BioMart

13 What we want to know about the gene BioMart

14 Choose a gene set by region, gene ID… BioMart

15 What are the gene IDs of all mouse protein coding genes on chromosome 10? An example:

16 What are the gene IDs of all mouse protein coding genes on chromosome 10? An example: Attributes: what we want to know: Gene IDs Filters: What we know: Mouse genes Protein coding Chromosome 10

17 Change dataset to mouse An example:

18 Click on Attributes to choose what we want to know

19 An example: Click on gene and select gene ID

20 An example: Click on Filters Expend region

21 An example: Choose chromosome 10

22 An example: Expend Gene

23 An example: Select Gene type: Protein coding

24 An example: Click on Results

25 An example:



28 Sequences: UTRs, flanking sequences, cDNA and peptides, etc Gene IDs from Ensembl and external sources (MGI, Entrez, etc.) Microarray data Protein Functions/descriptions (Interpro, GO) Orthologous gene sets SNP/ Variation Data What else can we do with BioMart?

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